void DmetEngine::defineStates() { defineOption("", "num-rows", PgOpt::INT_OPT, "The number of rows on the chip.", "-1"); defineOption("", "num-cols", PgOpt::INT_OPT, "The number of cols on the chip.", "-1"); defineOption("", "probe-count", PgOpt::INT_OPT, "The number of probes on the chip.", "-1"); }
/** * @brief Define the options used by the log2 ratio engine. */ void CNReferenceEngine::defineOptions() { defineOptionSection("Input Options"); defineOption("","expr-summary-file", PgOpt::STRING_OPT, "Expression Summary Table file.", ""); defineOption("","genotype-calls-file", PgOpt::STRING_OPT, "Genotype Calls Table file.", ""); defineOption("","genotype-confidences-file", PgOpt::STRING_OPT, "Genotype Confidences Table file.", ""); defineOption("","genotype-report-file", PgOpt::STRING_OPT, "Genotype Report Table file.", ""); // defOptMult("", "genotype-chp-file", PgOpt::STRING_OPT, "Genotype CHP file.", ""); // defineOption("","chrRefId", PgOpt::INT_OPT, // "Reference Chromosome", // "2"); defineOption("","reference-file", PgOpt::STRING_OPT, "Copy Number Reference file.", ""); defineOptionSection("Output Options"); defineOption("","reference-text-output", PgOpt::BOOL_OPT, "Output the reference-file in acii text format.", "false"); defineOptionSection("Analysis Options"); defineOption("", "log2-input", PgOpt::BOOL_OPT, "Input Allele Summaries are in log2.", "false"); defineOption("", "adapter-type-normalization", PgOpt::BOOL_OPT, "Adapter Type Normalization option. true = perform adapter type normalization.", "true"); defineOptionSection("Advanced Options"); defineOption("", "set-analysis-name", PgOpt::STRING_OPT, "Analysis name to use as prefix for output files.", ""); defineOptionSection("Execution Control Options"); defineOption("", "mem-usage", PgOpt::INT_OPT, "How many MB of memory to use for this run.", "0"); defineSharedOptions(); }
int main(int argc, char *argv[]) { QApplication a(argc, argv); SQArgDescMap optionDesc; QMap<QString, QVariant> option; if (argc < 2) { std::cerr << "Too few arguments, syntax is : -sub subfile videofile" << std::endl; return 1; } sq_add_gsttoyunda_plugin_path(qApp->applicationDirPath()); try { QGst::init(&argc, &argv); } catch (QGlib::Error qgerr) { std::cerr << "Can't init gstreamer" << std::endl; return 1; } qInstallMessageHandler(myMessageOutput); defineOption(optionDesc); QStringList arg = a.arguments(); arg.removeFirst(); bool vopt = SQArg::fillWithDesc(option, arg, optionDesc); if (vopt == false) return 1; VideoPlayer w(""); qDebug() << option["base_image_path"].toString(); if (!option["base_image_path"].toString().isEmpty()) w.setToyundaImagePath(option["base_image_path"].toString()); std::cout << "Subtitle file : " << option["subtitle"].toString().constData() << std::endl; std::cout << "Video File : " << arg[0].constData() << std::endl; w.setVideoFile(arg[0]); w.setSubFile(option["subtitle"].toString()); w.show(); w.play(); w.show(); return a.exec(); }
int runMoc(int argc, char **argv) { QCoreApplication app(argc, argv); QCoreApplication::setApplicationVersion(QString::fromLatin1(QT_VERSION_STR)); bool autoInclude = true; bool defaultInclude = true; Preprocessor pp; Moc moc; pp.macros["Q_MOC_RUN"]; pp.macros["__cplusplus"]; // Don't stumble over GCC extensions Macro dummyVariadicFunctionMacro; dummyVariadicFunctionMacro.isFunction = true; dummyVariadicFunctionMacro.isVariadic = true; dummyVariadicFunctionMacro.arguments += Symbol(0, PP_IDENTIFIER, "__VA_ARGS__"); pp.macros["__attribute__"] = dummyVariadicFunctionMacro; pp.macros["__declspec"] = dummyVariadicFunctionMacro; QString filename; QString output; QFile in; FILE *out = 0; // Note that moc isn't translated. // If you use this code as an example for a translated app, make sure to translate the strings. QCommandLineParser parser; parser.setApplicationDescription(QStringLiteral("Qt Meta Object Compiler version %1 (Qt %2)") .arg(mocOutputRevision).arg(QString::fromLatin1(QT_VERSION_STR))); parser.addHelpOption(); parser.addVersionOption(); QCommandLineOption outputOption(QStringLiteral("o")); outputOption.setDescription(QStringLiteral("Write output to file rather than stdout.")); outputOption.setValueName(QStringLiteral("file")); parser.addOption(outputOption); QCommandLineOption includePathOption(QStringLiteral("I")); includePathOption.setDescription(QStringLiteral("Add dir to the include path for header files.")); includePathOption.setValueName(QStringLiteral("dir")); parser.addOption(includePathOption); QCommandLineOption macFrameworkOption(QStringLiteral("F")); macFrameworkOption.setDescription(QStringLiteral("Add Mac framework to the include path for header files.")); macFrameworkOption.setValueName(QStringLiteral("framework")); parser.addOption(macFrameworkOption); QCommandLineOption preprocessOption(QStringLiteral("E")); preprocessOption.setDescription(QStringLiteral("Preprocess only; do not generate meta object code.")); parser.addOption(preprocessOption); QCommandLineOption defineOption(QStringLiteral("D")); defineOption.setDescription(QStringLiteral("Define macro, with optional definition.")); defineOption.setValueName(QStringLiteral("macro[=def]")); parser.addOption(defineOption); QCommandLineOption undefineOption(QStringLiteral("U")); undefineOption.setDescription(QStringLiteral("Undefine macro.")); undefineOption.setValueName(QStringLiteral("macro")); parser.addOption(undefineOption); QCommandLineOption metadataOption(QStringLiteral("M")); metadataOption.setDescription(QStringLiteral("Add key/value pair to plugin meta data")); metadataOption.setValueName(QStringLiteral("key=value")); parser.addOption(metadataOption); QCommandLineOption noIncludeOption(QStringLiteral("i")); noIncludeOption.setDescription(QStringLiteral("Do not generate an #include statement.")); parser.addOption(noIncludeOption); QCommandLineOption pathPrefixOption(QStringLiteral("p")); pathPrefixOption.setDescription(QStringLiteral("Path prefix for included file.")); pathPrefixOption.setValueName(QStringLiteral("path")); parser.addOption(pathPrefixOption); QCommandLineOption forceIncludeOption(QStringLiteral("f")); forceIncludeOption.setDescription(QStringLiteral("Force #include <file> (overwrite default).")); forceIncludeOption.setValueName(QStringLiteral("file")); parser.addOption(forceIncludeOption); QCommandLineOption prependIncludeOption(QStringLiteral("b")); prependIncludeOption.setDescription(QStringLiteral("Prepend #include <file> (preserve default include).")); prependIncludeOption.setValueName(QStringLiteral("file")); parser.addOption(prependIncludeOption); QCommandLineOption noNotesWarningsCompatOption(QStringLiteral("n")); noNotesWarningsCompatOption.setDescription(QStringLiteral("Do not display notes (-nn) or warnings (-nw). Compatibility option.")); noNotesWarningsCompatOption.setValueName(QStringLiteral("which")); parser.addOption(noNotesWarningsCompatOption); QCommandLineOption noNotesOption(QStringLiteral("no-notes")); noNotesOption.setDescription(QStringLiteral("Do not display notes.")); parser.addOption(noNotesOption); QCommandLineOption noWarningsOption(QStringLiteral("no-warnings")); noWarningsOption.setDescription(QStringLiteral("Do not display warnings (implies --no-notes).")); parser.addOption(noWarningsOption); QCommandLineOption ignoreConflictsOption(QStringLiteral("ignore-option-clashes")); ignoreConflictsOption.setDescription(QStringLiteral("Ignore all options that conflict with compilers, like -pthread conflicting with moc's -p option.")); parser.addOption(ignoreConflictsOption); parser.addPositionalArgument(QStringLiteral("[header-file]"), QStringLiteral("Header file to read from, otherwise stdin.")); parser.addPositionalArgument(QStringLiteral("[@option-file]"), QStringLiteral("Read additional options from option-file.")); const QStringList arguments = argumentsFromCommandLineAndFile(app.arguments()); parser.process(arguments); const QStringList files = parser.positionalArguments(); if (files.count() > 1) { error("Too many input files specified"); parser.showHelp(1); } else if (!files.isEmpty()) { filename = files.first(); } const bool ignoreConflictingOptions = parser.isSet(ignoreConflictsOption); output = parser.value(outputOption); pp.preprocessOnly = parser.isSet(preprocessOption); if (parser.isSet(noIncludeOption)) { moc.noInclude = true; autoInclude = false; } if (!ignoreConflictingOptions) { if (parser.isSet(forceIncludeOption)) { moc.noInclude = false; autoInclude = false; foreach (const QString &include, parser.values(forceIncludeOption)) { moc.includeFiles.append(QFile::encodeName(include)); defaultInclude = false; } } foreach (const QString &include, parser.values(prependIncludeOption)) moc.includeFiles.prepend(QFile::encodeName(include)); if (parser.isSet(pathPrefixOption)) moc.includePath = QFile::encodeName(parser.value(pathPrefixOption)); }
int main(int ac, char *ag[]) { QToyunda *toyunda; QApplication *qapp; SQArgDescMap optionDesc; QMap<QString, QVariant> option; QDebugErrorHandler *errorHandler; errorHandler = new QDebugErrorHandler(); defineOption(optionDesc); qapp = new QApplication(ac, ag); // Handle arguments QStringList arg = qapp->arguments(); arg.removeFirst(); bool vopt = SQArg::fillWithDesc(option, arg, optionDesc); // Help if (option["help"].toBool() || vopt == false) { QTextStream cout(stdout); cout << "QToyunda\nSynopsis : "; cout << "./qtoyunda --player playername --renderer renderername --video videofile --subtitle subtitlefile\n\n"; cout.flush(); if (option["help"].toBool()) { cout << "All option available :\n"; cout.flush(); SQArg::generateLongHelp(optionDesc); return 0; } return 1; } // Player and renderer option QStringList playerOption; if (!option["playeroption"].toString().isEmpty()) playerOption = option["playeroption"].toString().split(","); QStringList rendererOption; if (!option["rendereroption"].toString().isEmpty()) rendererOption = option["rendereroption"].toString().split(","); rendererOption << "logo=:/main/Toyunda logo.png"; qDebug() << rendererOption; toyunda = new QToyunda(errorHandler); toyunda->setPlayerName(option["player"].toString()); toyunda->setRendererName(option["renderer"].toString()); toyunda->setPlayerOption(playerOption); toyunda->setRendererOption(rendererOption); QDir pluginPath = qApp->applicationDirPath(); pluginPath.cd("plugins"); toyunda->setPluginDirectory(pluginPath); toyunda->loadPlugins(); // FIXME playeroptionhelp and roh must not depend and toyunda if (option["playeroptionhelp"].toBool()) { toyunda->showPlayerOption(); return 0; } if (option["rendereroptionhelp"].toBool()) { toyunda->showRendererOption(); return 0; } qDebug() << "Init toyunda"; if (!toyunda->init()) { qCritical() << "Can't init qtoyunda, abord"; return 1; } qDebug() << "Load files"; toyunda->load(option["video"].toString(), option["subtitle"].toString()); qDebug() << "Play the video"; toyunda->play(); toyunda->showRenderer(); int ret = qapp->exec(); toyunda->dispose(); return ret; }
void DmetEngine::defineOptions() { defineOptionSection("Input Options"); defineOption("", "cel-files", PgOpt::STRING_OPT, "Text file specifying cel files to process, one per line with the first line being 'cel_files'.", ""); defineOption("c", "cdf-file", PgOpt::STRING_OPT, "File defining probe sets. Use either --cdf-file or --spf-file. ", ""); defineOption("", "spf-file", PgOpt::STRING_OPT, "File defining probe sets in spf (simple probe format) which is like a text cdf file.", ""); defineOption("", "special-snps",PgOpt::STRING_OPT, "File containing all snps of unusual copy (chrX,mito,Y)", ""); defineOption("", "chrX-probes", PgOpt::STRING_OPT, "File containing probe_id (1-based) of probes on chrX. " "Used for copy number probe chrX/Y ratio gender calling. ", ""); defineOption("", "chrY-probes", PgOpt::STRING_OPT, "File containing probe_id (1-based) of probes on chrY. " "Used for copy number probe chrX/Y ratio gender calling. ", ""); defineOption("", "reference-input", PgOpt::STRING_OPT, "Reference file with cluster prior information. ", ""); defineOption("s", "probeset-ids", PgOpt::STRING_OPT, "Tab delimited file with column 'probeset_id' specifying probesets to analyze.", ""); defineOption("", "probeset-ids-reported", PgOpt::STRING_OPT, "Tab delimited file with column 'probeset_id' specifying probesets to report. " "This should be a subset of those specified with --probeset-ids if that option is used.", ""); defOptMult("", "chip-type", PgOpt::STRING_OPT, "Chip types to check library and CEL files against. " "Can be specified multiple times. " "The first one is propigated as the chip type in the output files. " "Warning, use of this option will override the usual check between chip types " "found in the library files and cel files. You should use this option instead " "of --force when possible. ", ""); defineOption("", "region-model", PgOpt::STRING_OPT, "Regions model parameters. ", ""); defineOption("", "probeset-model", PgOpt::STRING_OPT, "Probeset model parameters. ", ""); defineOption("", "cn-region-gt-probeset-file", PgOpt::STRING_OPT, "Tab delimited file mapping probeset ids to copynumber regions. ", ""); defineOptionSection("Output Options"); defineOption("", "cc-chp-output", PgOpt::BOOL_OPT, "Output resulting calls in directory called 'chp' under out-dir. " "This makes one AGCC Multi Data CHP file per cel file analyzed.", "false"); defineOption("", "reference-output", PgOpt::STRING_OPT, "File to write reference values to. Specifying this option will turn on " "dynamic clustering. WARNING: Currently the " "resulting reference file is not really usable as a reference. " "See the manual for more info. ", ""); defineOption("", "batch-name", PgOpt::STRING_OPT, "The name of the batch for the dynamic cluster analysis. ", ""); defineOptionSection("Analysis Options"); defineOption("", "set-analysis-name", PgOpt::STRING_OPT, "Explicitly set the analysis name. This affects output file names (ie prefix) and various meta info.", "dmet"); defineOption("", "ps-analysis", PgOpt::STRING_OPT, "Explicitly set the ProbesetSummarizeEngine analysis string.", ""); defineOption("", "gt-analysis", PgOpt::STRING_OPT, "Explicitly set the ProbesetGenotypeEngine analysis string.", ""); defineOption("", "gt-qmethod-spec", PgOpt::STRING_OPT, "Explicitly set the ProbesetGenotypeEngine quant spec.", ""); defineOption("", "sample-type", PgOpt::STRING_OPT, "Set the type of samples being processed. eg genomic, plasmid.", "unknown"); defineOption("", "batch-info", PgOpt::BOOL_OPT, "Indicates whether or not information about other cel files in the batch " "should be reported in CHP headers.", "false"); defineOption("", "null-context", PgOpt::BOOL_OPT, "Indicates whether or not context info should be populated in the CHP files.", "true"); defineOption("", "run-cn-engine", PgOpt::BOOL_OPT, "Indicates if the CN engine should be run or not.", "true"); defineOption("", "pra-thresh", PgOpt::INT_OPT, "The threshold for calling PRAs based on the cluster mean strength.", "3"); defineOption("", "geno-call-thresh", PgOpt::DOUBLE_OPT, "The confidence threshold for reporting calls in the CHP file.", "0.1"); defineOptionSection("Gender Options"); defineOption("", "female-thresh", PgOpt::DOUBLE_OPT, "Threshold for calling females when using cn-probe-chrXY-ratio method.", "0.17"); defineOption("", "male-thresh", PgOpt::DOUBLE_OPT, "Threshold for calling females when using cn-probe-chrXY-ratio method.", "0.68"); defineOptionSection("Advanced Options"); defineOption("", "call-coder-max-alleles", PgOpt::INT_OPT, "For encoding/decoding calls, the max number of alleles per marker to allow.", "6"); defineOption("", "call-coder-type", PgOpt::STRING_OPT, "The data size used to encode the call.", "UCHAR"); defineOption("", "call-coder-version", PgOpt::STRING_OPT, "The version of the encoder/decoder to use", "1.0"); defineOptionSection("Execution Control Options"); defineOption("", "use-disk", PgOpt::BOOL_OPT, "Store CEL intensities to be analyzed on disk.", "true"); defineOption("", "disk-cache", PgOpt::INT_OPT, "Size of intensity memory cache in millions of intensities (when --use-disk=true).", "50"); defineOptionSection("Engine Options (Not used on command line)"); defOptMult("", "cels", PgOpt::STRING_OPT, "Cel files to process.", ""); defOptMult("", "report", PgOpt::STRING_OPT, "Probesets to report. eg consented.", ""); }